We all know that is the fluids segregated by the X Factor between the Brain and the cerebelum of a mutant what causes them to have mutant powers (Remeber in X2 with Jason Striker, how Striker would use X Factor Fluid from his son to control , Lady Deathstrike, Nightcrawler, and Cyclops?). Thats how they made the cure, they use Leeche's X Factor Fluid to create this "antibody" that goes straight to the DNA of a mutant and changes it into Human DNA, I put quote on quote antibody because the principles used for this "cure" are the ones of a virus, lets be specific and mention the HIV virus which changes the human DNA in RNA which causes the human body to stop creating white cells in the blood (antibodies), just like this "cure" causes the X Factor to Stop producing X Factor Fluid...BUT it doesnt kill the X Factor, so eventually the X Factor as an organ that it is, will start producing X Fluid once the mutant inmune system catches up. Now this is not an atibody, they call it antibody in the movie because of the human point of view, but the "cure" is actually a virus genetically enginered from Leeche's X Factor fluid, so the "cure" condition is actually a mutant decease for what they would need a mutant vaccine for this and thats why the mutant inmune system cannot avoid this "antibody" rather called Mutant Virus. It's all behind the X Factor Fluids, thats the reason why they still need the boy to create it, they cant replicate X Factor Fluid. Seems like the only one to understand this was Storm:
"There is nothing to cure,
nothing's wrong with any of us
for that matter"
Mutations is just that, mutation, not a decease.